Re: Fix to R package
I noticed that gcc-4.2.0 was updated as of yesterday, so I rebuilt it then tried to rebuild the R package again but unfortunately it still fails to build. I noticed during the compilation that the -fPIC option seems to be included with some of the gcc compiling but when it starts to compile the libgfortran I don't see the -fPIC option anymore. It seems that perhaps the compilation excludes the -fPIC option when building libgfortran which seems to be related with R not building. I don't really know much more than this because as I'm sure you can tell, I am no C programmer. Any help with this is appreciated. Thanks. On Thu, 2007-06-28 at 12:19 -0700, David Fetter wrote: > It seems that the problem with building the R package on an amd64 bit > platform may be a gcc4 problem. See here: > "http://www.gentoo.org/proj/en/base/amd64/howtos/index.xml?part=1&chap=3#doc_chap5";. > I'm working on testing this theory out, but ultimately, it seems that a > flag to add -fPic explicitly for amd64 archs might be needed. > > On Wed, 2007-06-27 at 13:00 -0700, David Fetter wrote: > > Ah, shoot! I was hoping the patches would fix our 64-bit problem with R > > not compiling. :-( I'm getting the following error when I try to > > compile it: > > > > /usr/local/bin/cc -std=gnu99 -I. -I../../../src/include > > -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic > > -fPIC -c Lapack.c -o Lapack.o > > /usr/local/bin/cc -std=gnu99 -shared -L/usr/local/lib -o lapack.so > > Lapack.o -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran > > -lm /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortranbegin.a > > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a > > /usr/local/bin/ld: skipping > > incompatible > > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a when > > searching for -lgfortran > > /usr/local/bin/ld: > > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a(pow_i4_i4.o): > > relocation R_X86_64_32 against `a local symbol' can not be used when > > making a shared object; recompile with -fPIC > > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a: > > could not read symbols: Bad value > > collect2: ld returned 1 exit status > > make[4]: *** [lapack.so] Error 1 > > make[3]: *** [R] Error 2 > > make[2]: *** [R] Error 1 > > make[1]: *** [R] Error 1 > > make: *** [R] Error 1 > > > > > > On Wed, 2007-06-27 at 20:07 +0200, Ralf S. Engelschall wrote: > > > On Wed, Jun 27, 2007, Dennis McRitchie wrote: > > > > > > > I just uploaded a modified spec file for the R statistical package. > > > > > > > > The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR, > > > > but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to > > > > allow packages to be installed. > > > > > > Now fixed in the latest "r" package of OpenPKG CURRENT -- together with > > > another packaging bug. Thanks for your feedback and support. > > > > > >Ralf S. Engelschall > > >[EMAIL PROTECTED] > > >www.engelschall.com > > > > > > __ > > > OpenPKG http://openpkg.org > > > Developer Communication List openpkg-dev@openpkg.org > > > -- David Fetter - Portland State University - UNIX Systems Administrator "Great minds discuss ideas; average minds discuss events; small minds discuss people." ~Eleanor Roosevelt signature.asc Description: This is a digitally signed message part
Re: Fix to R package
It seems that the problem with building the R package on an amd64 bit platform may be a gcc4 problem. See here: "http://www.gentoo.org/proj/en/base/amd64/howtos/index.xml?part=1&chap=3#doc_chap5";. I'm working on testing this theory out, but ultimately, it seems that a flag to add -fPic explicitly for amd64 archs might be needed. On Wed, 2007-06-27 at 13:00 -0700, David Fetter wrote: > Ah, shoot! I was hoping the patches would fix our 64-bit problem with R > not compiling. :-( I'm getting the following error when I try to > compile it: > > /usr/local/bin/cc -std=gnu99 -I. -I../../../src/include > -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic > -fPIC -c Lapack.c -o Lapack.o > /usr/local/bin/cc -std=gnu99 -shared -L/usr/local/lib -o lapack.so > Lapack.o -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran > -lm /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortranbegin.a > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a > /usr/local/bin/ld: skipping > incompatible /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a > when searching for -lgfortran > /usr/local/bin/ld: > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a(pow_i4_i4.o): > relocation R_X86_64_32 against `a local symbol' can not be used when making > a shared object; recompile with -fPIC > /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a: > could not read symbols: Bad value > collect2: ld returned 1 exit status > make[4]: *** [lapack.so] Error 1 > make[3]: *** [R] Error 2 > make[2]: *** [R] Error 1 > make[1]: *** [R] Error 1 > make: *** [R] Error 1 > > > On Wed, 2007-06-27 at 20:07 +0200, Ralf S. Engelschall wrote: > > On Wed, Jun 27, 2007, Dennis McRitchie wrote: > > > > > I just uploaded a modified spec file for the R statistical package. > > > > > > The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR, > > > but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to > > > allow packages to be installed. > > > > Now fixed in the latest "r" package of OpenPKG CURRENT -- together with > > another packaging bug. Thanks for your feedback and support. > > > >Ralf S. Engelschall > >[EMAIL PROTECTED] > >www.engelschall.com > > > > __ > > OpenPKG http://openpkg.org > > Developer Communication List openpkg-dev@openpkg.org > > -- David M. Fetter - Portland State University - UNIX Systems Administrator "Reality is merely an illusion, albeit a very persistent one." ~Einstein signature.asc Description: This is a digitally signed message part
Re: Fix to R package
Ah, shoot! I was hoping the patches would fix our 64-bit problem with R not compiling. :-( I'm getting the following error when I try to compile it: /usr/local/bin/cc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -fPIC -c Lapack.c -o Lapack.o /usr/local/bin/cc -std=gnu99 -shared -L/usr/local/lib -o lapack.so Lapack.o -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran -lm /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortranbegin.a /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a /usr/local/bin/ld: skipping incompatible /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a when searching for -lgfortran /usr/local/bin/ld: /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a(pow_i4_i4.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[4]: *** [lapack.so] Error 1 make[3]: *** [R] Error 2 make[2]: *** [R] Error 1 make[1]: *** [R] Error 1 make: *** [R] Error 1 On Wed, 2007-06-27 at 20:07 +0200, Ralf S. Engelschall wrote: > On Wed, Jun 27, 2007, Dennis McRitchie wrote: > > > I just uploaded a modified spec file for the R statistical package. > > > > The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR, > > but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to > > allow packages to be installed. > > Now fixed in the latest "r" package of OpenPKG CURRENT -- together with > another packaging bug. Thanks for your feedback and support. > >Ralf S. Engelschall >[EMAIL PROTECTED] >www.engelschall.com > > __ > OpenPKG http://openpkg.org > Developer Communication List openpkg-dev@openpkg.org > -- David M. Fetter - Portland State University - UNIX Systems Administrator "Reality is merely an illusion, albeit a very persistent one." ~Einstein signature.asc Description: This is a digitally signed message part
Re: Fix to R package
On Wed, Jun 27, 2007, Dennis McRitchie wrote: > I just uploaded a modified spec file for the R statistical package. > > The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR, > but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to > allow packages to be installed. Now fixed in the latest "r" package of OpenPKG CURRENT -- together with another packaging bug. Thanks for your feedback and support. Ralf S. Engelschall [EMAIL PROTECTED] www.engelschall.com __ OpenPKG http://openpkg.org Developer Communication List openpkg-dev@openpkg.org
Fix to R package
I just uploaded a modified spec file for the R statistical package. The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR, but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to allow packages to be installed. Dennis Dennis McRitchie Computational Science and Engineering Support (CSES) Academic Services Department Office of Information Technology Princeton University __ OpenPKG http://openpkg.org Developer Communication List openpkg-dev@openpkg.org
